[Biopython-dev] [Bug 3060] Add ungap method to the SeqRecord?

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3060


biopython-bugzilla at maubp.freeserve.co.uk changed:

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------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2010-06-22 10:58 EST -------
(From update of attachment 1482)
(In reply to comment #3)
> 
> I've been trying building SeqFeature objects for the reads in an ACE file,
> http://github.com/peterjc/biopython/tree/ace-reads
> 
> In this case when I call the SeqRecord ungap method, many of my read features
> are lost with the current implementation (because they included gaps). This
> also showed the ungap code to be quite slow for features. I'm going to have
> another look at this.

My new code handles SeqFeature ungapping so as to preserve all the features by
adjusting their end points. This is also much faster:

http://github.com/peterjc/biopython/tree/ungap2


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